DOCSLIB.ORG

Transcriptomic Analysis of Eruca Vesicaria Subs

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Transcriptomic Analysis of Eruca Vesicaria Subs Huang et al. BMC Plant Biology (2019) 19:419 https://doi.org/10.1186/s12870-019-1997-2 RESEARCH ARTICLE Open Access Transcriptomic analysis of Eruca vesicaria subs. sativa lines with contrasting tolerance to polyethylene glycol-simulated drought stress Bang-Lian Huang1,2, Xuan Li1, Pei Liu1, Lan Ma1, Wenhua Wu1, Xuekun Zhang3, Zaiyun Li4 and Bangquan Huang1* Abstract Background: Eruca vesicaria subsp. sativa is one of the Cruciferae species most tolerant to drought stress. In our previous study some extremely drought-tolerant/sensitive Eruca lines were obtained. However little is known about the mechanism for drought tolerance in Eruca. Methods: In this study two E. vesicaria subs. sativa lines with contrasting drought tolerance were treated with liquid MS/PEG solution. Total RNA was isolated from 7-day old whole seedlings and then applied to Illumina sequencing platform for high-throughput transcriptional sequencing. Results: KEGG pathway analysis indicated that differentially expressed genes (DEGs) involved in alpha-Linolenic acid metabolism, Tyrosine metabolism, Phenylalanine, Tyrosine and tryptophan biosynthesis, Galactose metabolism, Isoquinoline alkaloid biosynthesis, Tropane, Piperidine and pyridine alkaloid biosynthesis, Mineral absorption, were all up-regulated specifically in drought-tolerant (DT) Eruca line under drought stress, while DEGs involved in ribosome, ribosome biogenesis, Pyrimidine metabolism, RNA degradation, Glyoxylate and dicarboxylate metabolism, Aminoacyl-tRNA biosynthesis, Citrate cycle, Methane metabolism, Carbon fixation in photosynthetic organisms, were all down-regulated. 51 DEGs were found to be most significantly up-regulated (log2 ratio ≥ 8) specifically in the DT line under PEG treatment, including those for ethylene-responsive transcription factors, WRKY and bHLH transcription factors, calmodulin-binding transcription activator, cysteine-rich receptor-like protein kinase, mitogen- activated protein kinase kinase, WD repeat-containing protein, OPDA reductase, allene oxide cyclase, aquaporin, O- acyltransferase WSD1, C-5 sterol desaturase, sugar transporter ERD6-like 12, trehalose-phosphate phosphatase and galactinol synthase 4. Eight of these 51 DEGs wre enriched in 8 COG and 17 KEGG pathways. Conclusions: DEGs that were found to be most significantly up-regulated specifically in the DT line under PEG treatment, up-regulation of DEGs involved in Arginine and proline metabolism, alpha-linolenic acid metabolism and down-regulation of carbon fixation and protein synthesis might be critical for the drought tolerance in Eruca. These results will be valuable for revealing mechanism of drought tolerance in Eruca and also for genetic engineering to improve drought tolerance in crops. Keywords: Eruca vesicaria subs. Sativa, Genotypes, Drought tolerance, RNA-seq, Gene expression * Correspondence: [email protected] 1Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan 430062, China Full list of author information is available at the end of the article © The Author(s). 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Huang et al. BMC Plant Biology (2019) 19:419 Page 2 of 11 Background Table 1 Illumina RNA-Seq reads and de novo assembly statistics Drought is one of the most important environmental of Eruca transcriptome stresses in the world [1–3]. Previous studies indicated that Total number of raw reads 314,322,210 plant responses to drought stress is quite complicated and Total number of clean reads 254,660,002 exploring drought tolerance mechanism in plants is still a Mean length of reads (bp) 90 challenge [4–7]. Next generation sequencing (NGS) using Number of total unigenes 430,166 Illumina HiSeq2000 covers the transcriptome many folds and allows quantification of the detected transcripts [8, 9]. Mean length of unigenes (bp) 511.56 By using next generation sequencing the gene expression is Minimum unigene length (bp) 201 quantified, making it possible for quantitative comparisons Maximum unigene length (bp) 16,517 [10]. Many researchers have used transcriptome sequencing N50 (bp) 638 – to study the responses to drought stress in crops [10 16]. Unigenes annotated to Nr 139,090 Biological and genetic diversity exists among and within Unigenes annotated to KEGG 40,463 plant species regarding drought tolerance, however many of these adaptive mechanisms are not completely under- Unigenes annotated to COG 105,052 stood. Genome-wide identification of drought-responsive − transcriptions using genotypes with contrasting drought- value < 10 5)(Fig.1). Among the unigenes 83,392 had tolerance will help revealing interactions among metabolic identity between 22.86–80% and 55,698 higher than 80%. pathways in response to drought stress [12]. Eruca vesi- Regarding the species distribution, 83,034 unigene caria subsp. sativa is one of the Cruciferae species most (59.70%) had similarity between 19.32–80%, 56, 056 uni- tolerant to drought stress [17, 18]. In our previous study gene (40.30%) had similarity higher than 80%. Of the 139, some extremely drought-tolerant/sensitive Eruca lines were 090 unigenes annotated to Nr, 36,254 (26.06%) had obtained [19]. In this study, Illumina sequencing technology matches to sequences from Brassica napus, followed by was used to identify the differentially expressed genes that from Brassica rapa (27,894, 20.05%), Eutrema salsugi- (DEGs) and their biochemical pathways related to drought neum (5366, 3.86%), Hordeum vulgare (3578, 2.57%), Ara- tolerance in drought tolerant (DT) versus drought- bidopsis thaliana (3391, 2.44%), Physcomitrella patens susceptible (DS) Eruca genotypes. Expression level of some (3289, 2.36%), Camelina sativa (3249, 2.34%) (Fig. 2). selected drought-responsive genes was validated by using quantitative RT-PCR. To our knowledge,thisisthefirstre- COG annotation and enrichment port about the whole transcriptome analysis in E. vesicaria In total 105,052 unigenes were anotated to COG (Clusters subsp. sativa. The results provide transcriptome data valu- of Orthologous Groups of proteins) database and assigned able for understanding drought tolerance mechanism in to 25 COG functional clusters (Fig. 3), among which the Eruca and the differentially expressed genes could be valu- “general function prediction only” cluster comprised the able for improving drought tolerance in crops. highest number of unigenes (15,472, 14.73%), followed by the cluster “translation, ribosomal structure and biogen- Results esis” (14,062, 13.39%) and “Posttranslational modification, Overview of Illumina RNA sequencing and de novo protein turnover, chaperones” (10,244, 9.75%). By contrast, assembly of E. vesicaria subs. sativa transcriptome only 110 unigenes were classified into “Cell motility”,98 In total 314,322,210 raw reads after sequencing produced unigenes classified into “Nuclear structure” and 3 uni- 254,660,002 clean reads including 430,166 unique genes with genes classified into “Extracellular structures” (Fig. 3). N50 value of 638 bp and average length of 511.56 bp. The unigene length ranged from 201 to 16, 517 bp (Table 1). The unigenes included 94,463 clusters and 335,703 sin- GO anotation and enrichment gletons. Among the unigenes there were 308,310 (71.67%) GO (Gene ontology) with Nr annotation indicated that with length from 200 to 500 bp, 76,255 (17.73%) with 4953 unigenes were classified into 69 groups that could length from 500 bp to 1000 bp, 24,662 (5.73%) with length be categorized into three main classifications: “biological from 1000 bp to 1500 bp, 11,229 (2.61%) with length from process” (2859), “cellular component” (643) and “mo- 1500 bp to 2000 bp, 9709 (2.26%) with length longer than lecular function” (1451). In the “molecular function” 2000 bp, and no unigenes shorter than 200 bp (Table 2). class the largest number of unigenes (984) were involved Based on Nr annotation and the E-value distribution, it in “catalytic activity”; in the “cellular component” class was found that among the annotated unigenes 51,486 the largest number of unigenes (168) were involved in − (37.02%) shared very strong homology (E-value < 10 60), “cell part”; in the “biological process” class the largest − 31,700 (22.80%) had strong homology (10 60 <Evalue < number of unigenes (534) were involved in “metabolic − − 10 30) and 55, 904 (40.19%) showed homology (10 30 <E- process” (Additional file 1). Huang et al. BMC Plant Biology (2019) 19:419 Page 3 of 11 Table 2 Length distribution of the Unigenes Length (nt) Total < 200 200–500 500–1000 1000–1500 1500–2000 ≥2000 Number of Unigenes 430,166 0 308,310 76,255 24,662 11,229 9709 % 100 0.00 71.67 17.73 5.73 2.61 2.26 KEGG pathway annotation and unigene enrichment metabolism, 39 in Plant hormone signal transduction, 21 In total 28,295 unigenes were annotated to 344 KEGG path- in Phenylpropanoid biosynthesis, 13 in alpha-Linolenic ways (Additional file 2). The number of unigenes in different acid metabolism and 41 in D-Glutaminehe
Load more

Recommended publications
  • Removal of Heavy Metals from a Contaminated Soil Using Phytoremediation
    MATEC Web of Conferences 305, 00061 (2020) https://doi.org/10.1051/matecconf/202030500061 SESAM 2019 Removal of heavy metals from a contaminated soil using phytoremediation Georgiana Luiza Arnold Tatu, Nicolae Valentin Vladut, Iulian Voicea, Nicoleta Alexandra Vanghele, and Mirabela Augustina Pruteanu*, National Research - Development Institute for Machines and Installations Designed to Agriculture and Food Industry, 6 Ion Ionescu De La Brad Blv., 013813 Bucharest, Sector 1, Romania Abstract. Environment pollution with heavy metals, can be a cause of the industrialization activities and technological processes, and has become an important issue. Soil contamination due to natural or anthropogenic causes (such as mining, smelting, warfare and military training, electronic industries, fossil fuel consumption, waste disposal, agrochemical use and irrigation) is a major environmental hazard. Various remediation techniques have been highlighted to clean or restore soils contaminated with heavy metals such physical, chemical or biological. Phytoremediation is a relatively new approach to removing contaminants from the environmental. It may be defined as the use of plants to remove, destroy or sequester hazardous substances from environmental. This paper is a review of removal of heavy metals from a contaminated soil using phytoremediation. 1 Introduction Brassicaceae is one of the largest angiosperm families, predominant in the temperate region and best cultivated around the Mediterranean. They belong to a group of natural plants conduplicate cotyledons (rare acumbent or existing) and the segment (rare lomentaceous or nucciform) fruit, usually in general, tanks and have flowers with four petals of equal size in the shape of a cross "crucifer" [1-5]. The Brassicaceae family can have a large number of genres and species: ranging from 338 to 380 genres and from 2500 to ca.
    [Show full text]
  • 14/ 20176 EXTRAPOLATION TABLE for EFFECTIVENESS of FUNGICIDES ► DISEASES on VEGETABLE BRASSICAS
    14/ 20176 EXTRAPOLATION TABLE for EFFECTIVENESS of FUNGICIDES ► DISEASES ON VEGETABLE BRASSICAS INTRODUCTION The table provides detailed lists of acceptable extrapolations organized by crop groups, for regulatory authorities and applicants, in the context of the registration of plant protection products for minor uses. The table should be used in conjunction with the EPPO Standard PP1/257(1) - Efficacy and crop safety extrapolations for minor uses. It is important to ensure that expert judgment and regulatory experience are employed when using these tables. EPPO excludes liability as to the reliability of the information provided through these tables. The scope for extrapolation may be extended as data and experience with a certain plant protection products increases. The applicant should always provide appropriate justification and information to support the proposed extrapolation. For example, comparability of target biology may be a relevant factor, either in extrapolating to other target species or for the same target onto another crop. For crops, factors such as comparable growth habit, structure etc. should be considered. TABLE FORMAT The main pest species for the crop group are listed in Column 1 (although this is not exhaustive), and the pest group to which they belong is specified in Column 2. Companies may choose if they wish to provide data only for individual named species, which would then appear individually listed on the label. But underlined species have been identified as key major targets and as such it is advisable to generate data on these. Furthermore, data on these species then allow a claim to be made for the whole pest group (as specified in Column 2), if required.
    [Show full text]
  • Phyllotreta Cruciferae Striped Flea Beetle
    Flea Beetle Management in Brassica Greens Ruth Hazzard, Caryn Andersen, Roy Van Driesche, Francis Mangan University of Massachusetts Crucifer Flea Beetle • Predominant flea beetle species in this area • Solid black in color, with metallic sheen • Feeds only on brassicas • Introduced to America in the 1900’s • Scientific name: Phyllotreta cruciferae Striped Flea Beetle • Much less numerous in New England • Black with one yellow stripe down each wing cover • Emerges slightly earlier • Feeds only on brassicas • Scientific name: Photo courtesy of Manitoba Agriculture and Food Phyllotreta striolata Host Crops for Crucifer and Striped Flea Beetle Brassica oleracea Broccoli, Brussels Sprouts, Cabbage, Cauliflower, Kale, Collards, White- flowering Chinese Broccoli, Gai Lan Brassica rapa Chinese cabbage, Turnip, Hon Tsai Tai, Yellow-flowering Chinese Broccoli, Broccoli Raab, Komatsuna, Pac Choi, Tat Soi Brassica juncea Mustard Greens, Bok Choy Brassica nigra Black Mustard Brassica napus Red Russian Kale, Rutabaga, Oilseed rape, Canola Brassica campestris Canola, Turnip Raphanus sativus Radish, Daikon Eruca vesicaria Arugula Host Crops for Crucifer and Striped Flea Beetle Brassica oleracea Broccoli, Brussels Sprouts, Cabbage, Cauliflower, Kale, Collards, White-flowering Chinese Broccoli, Gai Lan Brassica rapa Chinese cabbage, Turnip, Hon Tsai Tai, Yellow-flowering Chinese Broccoli, Broccoli Raab, Komatsuna, Pac Choi, Tat Soi Brassica juncea Mustard Greens, Bok Choy Brassica nigra Black Mustard Brassica napus Red Russian Kale, Rutabaga, Oilseed rape,
    [Show full text]
  • Comparative Effects of Organic and Conventional Cropping Systems on Trace Elements Contents in Vegetable Brassicaceae: Risk Assessment
    applied sciences Article Comparative Effects of Organic and Conventional Cropping Systems on Trace Elements Contents in Vegetable Brassicaceae: Risk Assessment Fernando Cámara-Martos 1 , Jesús Sevillano-Morales 1, Luis Rubio-Pedraza 2, Jesús Bonilla-Herrera 2 and Antonio de Haro-Bailón 3,* 1 Departamento de Bromatología y Tecnología de los Alimentos, Campus Universitario de Rabanales, Universidad de Córdoba, Edificio C-1, 14014 Córdoba, Spain; [email protected] (F.C.-M.); [email protected] (J.S.-M.) 2 Departamento de Agricultura, Ayuntamiento de Alcalá la Real, 23680 Alcalá la Real (Jaén), Spain; [email protected] (L.R.-P.); [email protected] (J.B.-H.) 3 Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible (IAS–CSIC), Alameda del Obispo s/n, 14004 Córdoba, Spain * Correspondence: [email protected]; Tel.: +34-957-499235; Fax: +34-957-499252 Abstract: Genotypes selected from 3 plant species (Brassica rapa, Eruca vesicaria and Sinapis alba) belonging to the Brassicaceae family were chosen to compare the concentrations of 9 inorganic el- ements (Cd, Co, Cr, Cu, Fe, Ni, Mn, Pb and Zn) in these varieties, that were grown under both conventional and organic conditions during two agricultural seasons (2018/2019 and 2019/2020) on two different experimental farms (Farm I and Farm II). We found that, together with agriculture practices, the inorganic element concentrations in Brassicas depended on many other factors, includ- ing soil characteristics. However, there were no conclusive results indicating a lower heavy metal content or a higher nutritionally beneficial trace elements content in vegetables grown under organic Citation: Cámara-Martos, F.; agriculture. Finally, a probabilistic assessment (@Risk) derived from the consumption of 150–200 g Sevillano-Morales, J.; Rubio-Pedraza, of these vegetables showed that organic Brassicas fulfill in comparison with the conventional ones, L.; Bonilla-Herrera, J.; de Haro-Bailón, similar Dietary Reference Intakes (DRI) percentages for Co, Cr, Cu, Fe, Mn and Zn.
    [Show full text]
  • Antibacterial Activity of Italic Leaves Aqueous Extract Against Two Pathogenic Bacteria
    Salih et al (2020): Antibacterial activity of Italic leaves January 2020 Vol. 23 (I) Antibacterial activity of Italic leaves Aqueous Extract Against Two Pathogenic Bacteria Aml Hendi Salih1 Rajaa Hendi Salih2 Madeha H. Hussain 3 Ali S. Hassoon 4* 1,3(Department of Pharmacy, Medical Institute Tech. Mansour / Middle Technical University/ Iraq) 2(Department of Biological Science, College of Science / Mustansiriyah University, Iraq) 4(Department of Soil and Water Techniques, Al-Musaib Tech. College/ Al-Furat Al-Awsat Technical University, Iraq) *Correspond Author: ALI S. HASSOON: [email protected], [email protected] Abstract This research was achieved to detect the antibacterial efficacy of Eruca Sativa leaves aqueous extract against Two pathogenic bacteria, Two bacterial isolates Escherichia coli and staphylococcus aureus were isolated from cases of infected wound were used in this study . The anti-bacterial efficacy of Eruca Sativa Italic leaves extract was detected by measuring the inhibition zone in millimeters in 3 plates and the average was considered. The results showed Eruca Sativa extract inhibit both bacterial spp and the mean inhibitory zone for S.aureus was 14.2 mm and for E.Coli was 9.0mm.the mean inhibitory zone of Ampicillin was 20mm for S.aureus and 21.3mm for E. coli distilled water shown no antibacterial activity. Keywords: Eruca Sativa, leaves aqueous extract, S. aureus, E. Coli How to cite this article: Salih AH, Salih RH, et al (202Antibacterial activity of Italic leaves aqueous extract Formatiert: Rechts against two pathogenic bacteria, Ann Trop Med & Pub Health; 23:S409. DOI: http://doi.org/10.36295/ASRO.2020.23123 Introduction Eruca sativa (syns.
    [Show full text]
  • Growing Brassicas Please Bear with Us, Be Patient and Sue Kraemer Understanding If Any Technical Glitches Master Gardener Pop-Up During Tonight’S Presentation
    2/28/21 A Note About Our Class Tonight We Master Gardeners are all volunteers, and while we have acquired basic Zoom skills, sometimes unforeseen technical issues arise. Class 7: Growing Brassicas Please bear with us, be patient and Sue Kraemer understanding if any technical glitches Master Gardener pop-up during tonight’s presentation. 1 2 Another note The information contained in Growing Groceries presentations is based on WSU home gardening publications and other science and research based materials. Resource lists are provided on the King County Growing Groceries website and at the end of some presentations. To enliven the learning experience, speakers may use examples from their own garden experience and draw from their personal gardening successes and failures. Photo Credit: Sue Kraemer 3 4 1 2/28/21 The Mustard Family (Brassicaceae/Cruciferae) Brassicaceae Includes Many Vegetables Photo Credit: Sue Kraemer • Arugula (Eruca vesicaria and • Horseradish (Armoracia rusticana) Diplotaxis tenuifolia) • Kale (Brassica oleracea) • Broccoli (Brassica oleracea) • Kohlrabi (Brassica oleracea) • Brussels sprouts (Brassica oleracea) • Mustard greens (Brassica juncea) • Cabbage (Brassica oleracea) • Pac Choi (Brassica rapa) • Cauliflower (Brassica oleracea) • Radish (Raphanus sativus) • Collards (Brassica oleracea) • Rutabaga (Brassica napus) • Sea kale (Crambe maritima) • Turnip (Brassica rapa) 5 6 Growing Brassicaceae Leafy Greens Arugula, Collard greens, Kale, and Mustard greens Graphic Credits: vox.com 7 8 2 2/28/21 Kale and Collards Kale
    [Show full text]
  • Effect of Pomegranate Juice and Fresh Leaves of Eruca Vesicaria on Testosterone Hormone Level in Blood Serum of Male Rabbits
    Sys Rev Pharm 2020;11(10):1211-1214 A multifaceted review journal in the field of pharmacy Effect of Pomegranate Juice and Fresh Leaves of Eruca vesicaria on Testosterone Hormone Level in Blood Serum of Male Rabbits *Seeham Ali Qasim, Abeer Salih Ali Dept. Biology-Coll. Sci, Mustansiriyeh University, Iraq Email: [email protected] ABSTRACT Plants have been used as a treatment for many diseases from ancient to our Keywords: Jarjeer, Testosterone hormone, Fertility times, it has a great source of different drugs that used for our health benefits. This study assessed the effects of diluted Punica granatum (P. granatum) juice Correspondence: and Eruca sativa (E. sativa) fresh leaves on testosterone hormone level in male Seeham Ali Qasim albino rabbits. Twenty-one rabbits their̕ s weight between 1500 - 1800g, divided Dept. Biology-Coll. Sci, Mustansiriyeh University, Iraq into 3 groups each group consisting of 7 rabbits for 30 days. Group1 as a control, Email: [email protected] group 2 received 500 ml of diluted Punica juice daily; group 3 received 350 g of fresh leaves of Eruca sativa. Blood samples were collected after and calibrated 15 and 30 days for testosterone hormone. Statistically significant increase in testosterone levels in group (2) (P. granatum) at day 15, 30 respectively with mean values (13.671±0.830 and 22.257±0.822) ng/ml when compared with the control mean value (9.771±0.368 and 9.500±0.490) ng/ml at same days. And also, there was a significant increase in testosterone levels in group (3) E. vesicaria with mean values (12.100± 0.551and 15.071±0.61) ng/ml at day 15 and 30 respectively compared with the control mean value (9.771±0.368 and 9.500±0.490) ng/ml at same days.
    [Show full text]
  • Analysis of Growth Physiology and Phytochemical Content of Eruca and Diplotaxis Cultivars Under Different Light and Temperature Regimes
    Analysis of growth physiology and phytochemical content of Eruca and Diplotaxis Cultivars under different light and temperature regimes Article Accepted Version Wagstaff, C. (2014) Analysis of growth physiology and phytochemical content of Eruca and Diplotaxis Cultivars under different light and temperature regimes. Acta Horticulturae, 1040. pp. 361-374. ISSN 0567-7572 doi: https://doi.org/10.17660/ActaHortic.2014.1040.49 Available at http://centaur.reading.ac.uk/27921/ It is advisable to refer to the publisher’s version if you intend to cite from the work. See Guidance on citing . Published version at: http://www.actahort.org/books/1040/1040_49.htm Identification Number/DOI: https://doi.org/10.17660/ActaHortic.2014.1040.49 <https://doi.org/10.17660/ActaHortic.2014.1040.49> Publisher: International Society for Horticultural Science All outputs in CentAUR are protected by Intellectual Property Rights law, including copyright law. Copyright and IPR is retained by the creators or other copyright holders. Terms and conditions for use of this material are defined in the End User Agreement . www.reading.ac.uk/centaur CentAUR Central Archive at the University of Reading Reading’s research outputs online Analysis of Growth Physiology and Phytochemical Content of Eruca and Diplotaxis Cultivars Under Different Light and Temperature Regimes Carol Wagstaff Department of Food and Nutritional Sciences, University of Reading, PO Box 226, Whiteknights, Reading, Berkshire, RG6 6AP, UK Abstract Rocket is a leafy brassicaceous salad crop that encompasses two major genera (Diplotaxis and Eruca) and many different cultivars. Rocket is a rich source of antioxidants and glucosinolates, many of which are produced as secondary products by the plant in response to stress.
    [Show full text]
  • Brassica Crops
    SCREENING OF HERBICIDES FOR SELECTIVE WEED CONTROL IN BRASSICACEOUS CROPS ED PEACHEY HORTICULTURE DEPARTMENT Brassicaceae vegetable food and seed Rhapanus sativa: common radish B. oleracea: broccoli, cabbage, cauliflower, kale, collards B. rapa: turnip, napa cab, bok choi, rapini B. napus: rutabaga, Russian kale Eruca vesicaria: arugula Willamette Valley, Western Oregon ~8,000 acres of vegetable seeds $50 million value ◦ 225 fields pinned in 2012 ◦ 156 fields in 2017 Pinning Map Brassica+ Seed Production in PNW Western Washington and Oregon ◦>90% of the European cabbage, Brussels sprouts, rutabaga and turnip seed for the world ◦20 – 30 % of radish, Chinese cabbage and other oriental Brassica vegetable crops. Brassica seed production- small acreage but high value crop. Special Seed Exclusion Labeling, Oregon “This seed was produced using one or more products for which the United States Environmental Protection Agency has not established pesticide residue tolerances. This seed, in whole, as sprouts, or in any form, may not be used for human consumption or animal feed. Failure to comply with this condition may violate the requirements of the Federal Food and Drug Administration, the Oregon Department of Agriculture, and other regulatory agencies.” Weed Control Challenges CROPS AND ROTATION CROPS In radish o Shepherdspurse curse o Any wild mustard or radish o Dogfennel o Bedstraw o Nightshades (trifluralin result) Squash (seed crop) in Radish Radish in Squash Crops and Their Weedy Relatives Mustards, Shepherdspurse in Radish! Radish in Radish!! Alternatives to herbicides? Cultivation technologies 1/13/2021 Hybrid radish seed with 2 male rows Research focus Dimethenamid-P (1993) R. sativa Fluroxypyr (1997) R. sativa Sulfentrazone (1991) ◦ B rapa, B.
    [Show full text]
  • Community Sequencing Program: Project Proposal
    The Top 20 Brassicales – Genomes & Transcriptomes Community Sequencing Program: Project Proposal Proposer’s Name: Rod A. Wing, Tom Mitchell-Olds, J. Chris Pires, M. Eric Schranz, Detlef Weigel, Stephen Wright Project Title: Empowering functional plant genomics with genomes and transcriptomes of the Top 20 Brassicales Proposal ID: 652 1 | P a g e The Top 20 Brassicales – Genomes & Transcriptomes A) Brief description: Abstract: The Brassicaceae constitute not only one of the most diverse plant families, but also one rich in agronomically important vegetable and oilseed crops. It has over 3700 species that grow in a wide range of environments and habitats. Several species have been domesticated: these include different cabbages, broccoli, turnip, rapeseed, horseradish, and several mustards. Brassicaceae include a number of species that are current and emerging biodiesel crops. Arabidopsis thaliana, arguably the world‟s most important and tractable plant experimental system, is also in this family. The strategy behind the current JGI proposal is to generate high quality genome and transcriptome data sets and associated analyses for the Top 20 Brassicales (18 Brassicaceae plus two outgroup species). The proposed assemblies, combined with presently available genome sequences as well as forthcoming sequences being generated by consortium members (several in collaboration with JGI) will allow us to perform a number of analyses, such as the identification of conserved noncoding sequences across the family, and genes and genomic regions subject to recurrent diversifying selection. More importantly, the proposed JGI data will empower our consortium members to launch numerous full genome sequencing projects aimed at finishing the Top 20 Brassicales, and beyond.
    [Show full text]
  • The Biological Activities of Arabis Alpina L. Subsp. Brevifolia (DC
    Open Chem., 2018; 16: 930–936 Research Article Open Access N. Balpinar* The biological activities of Arabis alpina L. subsp. brevifolia (DC.) Cullen against food pathogens https:// doi.org/10.1515/chem-2018-0104 contains many species (Arabidopsis, Brassica, Boechera, received February 15, 2018; accepted June 23, 2018. Thellungiella, Camelina, Raphanus and Arabis) that have Abstract: In this study, in vitro biological activities of economic, scientific and agricultural importance [1-3]. This both methanol and ethanol extracts of Arabis alpina family comprises 49 tribes, 325 genera and 3740 species subsp. brevifolia were investigated. Also, the phenolic which mainly spread in the temperate region of the world, components of this plant was examined in this study. and Turkey is extremely rich in terms of the diversity of The extracts were tested against the eight strains of this family, as well [4-6]. In the family, the genus of Arabis food pathogens for their antimicrobial activities by L. containing about 60 species is represented by 17 species utilizing minimum inhibitory concentration (MIC) and in the Flora of Turkey and the East Aegean Islands and by disc diffusion assay. The non-enzymatic antioxidant 22 species (24 taxa) in Turkey [7-9]. Arabis alpina L. in the activities were determined according to scavenging of mountain habitats of Anatolia, which is distributed on the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH). The the alpine habitats, so named alpine rock-cress, emerges phenolic compounds were analyzed by high performance as model species in the ecological and evolutionary liquid chromatography (HPLC). The main component was researches which have been conducted in recent years ellagic acid for the methanol extract of stem-leaf, rutin for [10,11].
    [Show full text]
  • Brassicaceae
    Wild Crucifer Species as Sources of Traits Wild Crucifer Species as Sources of Agronomic Traits The following guide to the wild germplasm of Brassica and allied crops reviews the potential of wild crucifers, particularly members of the tribe Brassiceae, as sources of agronomic traits. In addition to traditional breeding methods, interspecific and intergeneric transfer of genes governing qualitative and quantitative characters from wild allies to cultivated forms will be facilitated with various in vitro methods, such as somatic cell genetics and recombinant DNA techniques (See Guide Part III). Examples of genetic variability in potential agronomic traits of germplasms of Brassica and related genera (Tribe Brassiceae) will be presented under 14 sections. Data will be presented for all species in the Family. CONTENTS 1. GERMPLASM 1.1 Brassicaceae Species Checklist 1.2 North American Germplasm – Tribe Brassiceae 1.2.1 North American Ethnobotany 1.2.2 Weed and Crop Species in Canada 1.2.3 Weed and Crop Species in U.S.A. and Mexico 1.2.4 Invasives 2. MORPHOLOGICAL CHARACTERS 2.1 Hairs/Trichomes 2.2 Leaf Thickness/Waxiness 2.3 Petal Colour 2.4 Resistance to Pod Shattering 2.5 Growth Form and Geocarpy 2.6 Floral Structure 2.7 Fruit Type and Dispersal 2.8 Seed Size 2.9 Vegetative Reproduction 3. GENOME ARRANGEMENT 3.1 Chromosome Numbers 3.2 Genome Size 3.3 Genome Comparative Mapping 3.4 Cruciferae: Compendium of Trait Genetics 4. CHEMICAL TRAITS 4.1 Fatty Acids 4.2 Glucosinolates (mustard oil glucosides) 4.3 Phenolics 4.4 Secondary Metabolites/Floral Pigments 4.5 Anti-pest/Allelopathy 4.6 Flavonoids 4.7 Peroxidases 4.8 Tocopherols 4.9 Nectar Production Wild Crucifer Species as Sources of Traits 4.10 Mucilage 4.11 Cyanide 5.
    [Show full text]